TB-Profiler result

Run: ERR4813953
Summary

Run ID: ERR4813953

Sample name:

Date: 2024-10-03T17:59:31.923634

Number of reads: 3123345

Percentage reads mapped: 99.61

Median coverage: 98.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: RR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.13
lineage4.1 Euro-American None 0.88
lineage4.1.2 Euro-American None 0.89
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.88
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid
ethambutol
pyrazinamide pncA c.527dupG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin Assoc w R
pncA 2288714 c.527dupG frameshift_variant 0.13 pyrazinamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.9 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.92 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 656168 p.Ser435Ala missense_variant 0.88 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.85 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 764723 p.Phe452Leu missense_variant 0.13 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302638 c.-293G>C upstream_gene_variant 0.15 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.87 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.11 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.16 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448923 c.420C>T synonymous_variant 0.18 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.9 rifampicin
bedaquiline
fbiB 3642107 c.573G>A synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.92 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.83 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.14 streptomycin Not assoc w R